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Iron in PDB 3t63: Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

All present enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase:
1.13.11.3;

Protein crystallography data

The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3t63 was solved by V.M.Purpero, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.09 / 1.54
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.119, 140.618, 167.879, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 17.8

Iron Binding Sites:

The binding sites of Iron atom in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase (pdb code 3t63). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3t63:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3t63

Go back to Iron Binding Sites List in 3t63
Iron binding site 1 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe600

b:30.3
occ:0.40
O1 M:BME1 1.9 28.0 0.5
S2 M:BME1 2.2 28.7 0.5
O M:HOH1559 2.2 24.6 0.5
OH M:TYR462 2.2 23.9 1.0
NE2 M:HIS460 2.3 19.4 1.0
OH M:TYR408 2.5 27.2 1.0
CE1 M:HIS460 3.0 17.0 1.0
CZ M:TYR462 3.1 18.5 1.0
C1 M:BME1 3.1 28.6 0.5
CE2 M:TYR462 3.2 17.1 1.0
C2 M:BME1 3.4 28.0 0.5
CZ M:TYR408 3.4 19.5 1.0
CD2 M:HIS460 3.4 17.0 1.0
NH1 M:ARG457 3.7 15.9 1.0
CE2 M:TYR408 3.8 20.0 1.0
O M:HOH613 3.9 23.9 1.0
ND1 M:HIS460 4.2 15.6 1.0
CE1 M:TYR462 4.4 16.0 1.0
CE1 M:TYR408 4.4 18.6 1.0
CG M:HIS460 4.4 15.7 1.0
CG M:ARG457 4.5 14.5 1.0
CD2 M:TYR462 4.5 16.0 1.0
S2 M:BME542 4.8 37.6 0.5
OE1 M:GLN477 4.9 15.8 1.0
O A:HOH429 4.9 17.5 1.0
O M:HOH276 4.9 17.3 1.0
CZ M:ARG457 5.0 13.6 1.0
CD2 A:TYR16 5.0 20.8 1.0

Iron binding site 2 out of 3 in 3t63

Go back to Iron Binding Sites List in 3t63
Iron binding site 2 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe600

b:28.7
occ:0.40
O N:HOH1560 2.1 21.3 0.5
O1 N:BME1 2.2 30.8 0.5
OH N:TYR462 2.2 24.8 1.0
OH N:TYR408 2.3 23.7 1.0
NE2 N:HIS460 2.3 19.0 1.0
S2 N:BME1 2.4 30.4 0.5
CE1 N:HIS460 3.0 18.5 1.0
CZ N:TYR462 3.1 16.9 1.0
CE2 N:TYR462 3.1 16.2 1.0
CZ N:TYR408 3.2 18.6 1.0
C1 N:BME1 3.4 30.9 0.5
CD2 N:HIS460 3.5 17.5 1.0
C2 N:BME1 3.6 30.5 0.5
NH2 N:ARG457 3.8 15.4 1.0
CE2 N:TYR408 3.8 18.8 1.0
O N:HOH577 3.9 22.1 1.0
CE1 N:TYR408 4.1 18.6 1.0
ND1 N:HIS460 4.2 16.6 1.0
CE1 N:TYR462 4.4 15.0 1.0
CG N:HIS460 4.5 14.9 1.0
CD2 N:TYR462 4.5 14.7 1.0
CG N:ARG457 4.5 14.2 1.0
O N:HOH239 4.8 17.4 1.0
S2 N:BME540 4.8 52.0 0.5
O B:HOH272 4.9 19.0 1.0
OE1 N:GLN477 4.9 15.1 1.0

Iron binding site 3 out of 3 in 3t63

Go back to Iron Binding Sites List in 3t63
Iron binding site 3 out of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe600

b:29.5
occ:0.40
O1 O:BME1 1.5 37.5 0.5
O O:HOH1561 2.1 23.3 0.5
NE2 O:HIS460 2.3 18.5 1.0
S2 O:BME1 2.3 34.6 0.5
O1 O:BME1 2.3 34.4 0.5
OH O:TYR408 2.3 25.7 1.0
OH O:TYR462 2.3 26.5 1.0
C1 O:BME1 2.6 38.8 0.5
CE1 O:HIS460 3.0 17.3 1.0
CZ O:TYR462 3.2 19.3 1.0
CE2 O:TYR462 3.2 19.5 1.0
CZ O:TYR408 3.3 18.9 1.0
CD2 O:HIS460 3.4 18.1 1.0
C1 O:BME1 3.5 34.6 0.5
C2 O:BME1 3.6 39.9 0.5
C2 O:BME1 3.6 35.2 0.5
CE2 O:TYR408 3.8 19.7 1.0
NH1 O:ARG457 3.8 16.1 1.0
O O:HOH654 3.9 24.7 1.0
CE1 O:TYR408 4.2 19.4 1.0
ND1 O:HIS460 4.2 17.1 1.0
CG O:HIS460 4.5 15.7 1.0
CE1 O:TYR462 4.5 15.5 1.0
CD2 O:TYR462 4.5 16.9 1.0
CG O:ARG457 4.5 15.2 1.0
O O:HOH274 4.9 17.0 1.0
CD2 C:TYR16 4.9 23.0 1.0
OE1 O:GLN477 4.9 16.1 1.0
O C:HOH238 5.0 19.6 1.0
S2 O:BME1 5.0 41.0 0.5

Reference:

V.M.Purpero, J.D.Lipscomb. Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase To Be Published.
Page generated: Sun Dec 13 15:21:45 2020

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